1RMH | pdb_00001rmh

RECOMBINANT CYCLOPHILIN A FROM HUMAN T CELL

• PDB DOI: https://doi.org/10.2210/pdb1RMH/pdb

• Classification: ISOMERASE/ ISOMERASE SUBSTRATE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1995-07-31 Released: 1996-10-14 
• Deposition Author(s): Zhao, Y., Ke, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization.

Zhao, Y., Ke, H.

(1996) Biochemistry 35: 7356-7361

• PubMed: 8652511 
• DOI: https://doi.org/10.1021/bi9602775
• Primary Citation Related Structures: 
  1RMH


• PubMed Abstract: 
  

  The crystal structure of human recombinant cyclophilin A complexed with a substrate of succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (AAPF) has been determined and refined to an R-factor of 0.189 at 2.4 A resolution. The structure revealed only the cis form of the substrate bound to cyclophilin A in a stoichiometry of 1:1. This binding ratio is different from the structure of cyclophilin A complexed with the tetrapeptide N-acetyl-Ala-Ala-Pro-Ala-amidomethylcourmarin. Model docking revealed that the trans form of AAPF does not fit into the active site. The observation that only the trans cis form of AAPF binds to cyclophilin A implies that cyclophilin A predominantly catalyzes the trans to cis isomerization of a peptidylprolyl amide bond. On the basis of the structure, it is proposed that Arg55 hydrogen-bonds to the nitrogen to deconjugate the resonance of the prolyl amide bond and thus facilitates the cis-trans rotation.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.06 kDa 
• Atom Count: 2,644 
• Modeled Residue Count: 340 
• Deposited Residue Count: 340 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOPHILIN A	A, B	164	Homo sapiens	Mutation(s): 0  Gene Names: CYCLOPHILIN EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937 GTEx:  ENSG00000196262

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AAPF PEPTIDE SUBSTRATE	C, D	6	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.8	α = 90
b = 109.2	β = 90
c = 118.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-10-14 
Deposition Author(s): Zhao, Y., Ke, H.

Revision History  

• Version 1.0: 1996-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary